assembly_id	genome_id	genome_def	crispr_array_locus_merge	crispr_array_location_merge	crispr_locus_id	crispr_pred_method	array_in_prot	prot_within_array_20000	prot_in_genome	crispr_type_by_cas_prot	consensus_repeat	repeat_length	self-targeting_spacer_number	self-targeting_target_number	spacer_location	protospacer_location	repeat_type	spacer_locus_num	spacer_num	correct_crispr_type	genome_cas_prots	unknown_protein_around_crispr	L10	L10_domain	L9	L9_domain	L8	L8_domain	L7	L7_domain	L6	L6_domain	L5	L5_domain	L4	L4_domain	L3	L3_domain	L2	L2_domain	L1	L1_domain	R1	R1_domain	R2	R2_domain	R3	R3_domain	R4	R4_domain	R5	R5_domain	R6	R6_domain	R7	R7_domain	R8	R8_domain	R9	R9_domain	R10	R10_domain
GCF_009912795.1_ASM991279v1	NZ_CP047801	Staphylococcus aureus strain UP_248 chromosome, complete genome	1	71373-71564	1	CRT	no	DEDDh	DEDDh,csa3,cas3,DinG,WYL	Unclear	GGTGGGGCCCNCAACANAGANN	22	2	9	71452-71485|71452-71485|71452-71485|71452-71485|71452-71485|71452-71485|71452-71485|71452-71485|71507-71543	NZ_CP047801.1_338691-338658|NZ_CP047801.1_1096030-1096063|NZ_CP047801.1_1364065-1364098|NZ_CP047801.1_1397302-1397269|NZ_CP047801.1_1833299-1833266|NZ_CP047801.1_1908055-1908022|NZ_CP047801.1_2498818-2498785|NZ_CP047801.1_2640763-2640796|NZ_CP047801.1_1350835-1350871	NA	3	3	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|49aa|up_0|NZ_CP047801.1_70921_71068_+,NA|31aa|down_5|NZ_CP047801.1_76949_77042_+,NA|37aa|down_9|NZ_CP047801.1_80047_80158_+	NA|101aa|up_9|NZ_CP047801.1_59102_59405_+	COG4496, COG4496, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_8|NZ_CP047801.1_59587_60280_+	COG1646, COG1646, Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only]	NA|731aa|up_7|NZ_CP047801.1_60276_62469_+	TIGR01073, ATP-dependent_DNA_helicase_PcrA, ATP-dependent DNA helicase PcrA	NA|668aa|up_6|NZ_CP047801.1_62472_64476_+	PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated	NA|400aa|up_5|NZ_CP047801.1_64488_65688_+	COG4851, CamS, Protein involved in sex pheromone biosynthesis [General function prediction only]	NA|513aa|up_4|NZ_CP047801.1_65776_67315_-	TIGR02121, Osmoregulated_proline_transporter, sodium/proline symporter	NA|101aa|up_3|NZ_CP047801.1_67681_67984_+	PRK00034, gatC, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC	NA|486aa|up_2|NZ_CP047801.1_67985_69443_+	PRK00012, gatA, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA	NA|476aa|up_1|NZ_CP047801.1_69455_70883_+	PRK05477, gatB, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB	NA|49aa|up_0|NZ_CP047801.1_70921_71068_+	NA	NA|316aa|down_0|NZ_CP047801.1_71705_72653_+	PRK13337, PRK13337, putative lipid kinase; Reviewed	NA|454aa|down_1|NZ_CP047801.1_72733_74095_+	COG2265, TrmA, SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]	NA|177aa|down_2|NZ_CP047801.1_74264_74795_+	pfam11667, DUF3267, Putative zincin peptidase	NA|357aa|down_3|NZ_CP047801.1_75041_76112_+	PRK02406, PRK02406, DNA polymerase IV; Validated	DEDDh|185aa|down_4|NZ_CP047801.1_76178_76733_-	cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III	NA|31aa|down_5|NZ_CP047801.1_76949_77042_+	NA	NA|167aa|down_6|NZ_CP047801.1_77123_77624_-	COG1528, Ftn, Ferritin-like protein [Inorganic ion transport and metabolism]	NA|438aa|down_7|NZ_CP047801.1_77915_79229_+	COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]	NA|244aa|down_8|NZ_CP047801.1_79230_79962_+	COG3442, COG3442, Predicted glutamine amidotransferase [General function prediction only]	NA|37aa|down_9|NZ_CP047801.1_80047_80158_+	NA
GCF_009912795.1_ASM991279v1	NZ_CP047801	Staphylococcus aureus strain UP_248 chromosome, complete genome	2	431019-431098	1	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	CCCAACATAGAGAATTTCGTAAAGAA	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|43aa|up_8|NZ_CP047801.1_423577_423706_+,NA|49aa|up_3|NZ_CP047801.1_426742_426889_+,NA	NA|589aa|up_9|NZ_CP047801.1_421478_423245_+	PRK00476, aspS, aspartyl-tRNA synthetase; Validated	NA|43aa|up_8|NZ_CP047801.1_423577_423706_+	NA	NA|258aa|up_7|NZ_CP047801.1_423705_424479_+	COG1179, COG1179, Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]	NA|425aa|up_6|NZ_CP047801.1_424639_425914_-	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|141aa|up_5|NZ_CP047801.1_425998_426421_+	COG1959, COG1959, Predicted transcriptional regulator [Transcription]	NA|61aa|up_4|NZ_CP047801.1_426520_426703_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|49aa|up_3|NZ_CP047801.1_426742_426889_+	NA	NA|338aa|up_2|NZ_CP047801.1_427125_428139_-	TIGR03558, oxido_grp_1, luciferase family oxidoreductase, group 1	NA|381aa|up_1|NZ_CP047801.1_428448_429591_+	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]	NA|373aa|up_0|NZ_CP047801.1_429591_430710_+	PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed	NA|223aa|down_0|NZ_CP047801.1_431391_432060_+	sd00006, TPR, Tetratricopeptide repeat	NA|826aa|down_1|NZ_CP047801.1_432061_434539_+	TIGR01448, recD_rel, helicase, putative, RecD/TraA family	NA|877aa|down_2|NZ_CP047801.1_434881_437512_+	PRK00252, alaS, alanyl-tRNA synthetase; Reviewed	NA|87aa|down_3|NZ_CP047801.1_437574_437835_+	PRK05473, IreB-like, IreB family regulatory phosphoprotein	NA|143aa|down_4|NZ_CP047801.1_437838_438267_+	COG0816, COG0816, Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B	NA|103aa|down_5|NZ_CP047801.1_438281_438590_+	PRK13678, PRK13678, hypothetical protein; Provisional	NA|213aa|down_6|NZ_CP047801.1_438874_439513_+	COG4122, COG4122, Predicted O-methyltransferase [General function prediction only]	NA|308aa|down_7|NZ_CP047801.1_439515_440439_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|423aa|down_8|NZ_CP047801.1_440450_441719_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|208aa|down_9|NZ_CP047801.1_441718_442342_+	PRK05480, PRK05480, uridine/cytidine kinase; Provisional
GCF_009912795.1_ASM991279v1	NZ_CP047801	Staphylococcus aureus strain UP_248 chromosome, complete genome	3	946773-946865	2	CRISPRCasFinder	no	cas3	DEDDh,csa3,cas3,DinG,WYL	Unclear	AGTTATCAATTTATTGATTACTGTTTCTTA	30	0	0	NA	NA	NA	1	1	Unclear	DEDDh,csa3,cas3,DinG,WYL	NA,NA	NA|117aa|up_9|NZ_CP047801.1_936336_936687_-	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|246aa|up_8|NZ_CP047801.1_936789_937527_-	PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed	NA|168aa|up_7|NZ_CP047801.1_937526_938030_-	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional	NA|92aa|up_6|NZ_CP047801.1_938217_938493_-	COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]	NA|456aa|up_5|NZ_CP047801.1_938927_940295_-	PRK10867, PRK10867, signal recognition particle protein; Provisional	NA|111aa|up_4|NZ_CP047801.1_940320_940653_-	PRK00118, PRK00118, putative DNA-binding protein; Validated	NA|417aa|up_3|NZ_CP047801.1_940639_941890_-	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional	NA|1189aa|up_2|NZ_CP047801.1_941889_945456_-	COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	NA|244aa|up_1|NZ_CP047801.1_945602_946334_-	PRK00102, rnc, ribonuclease III; Reviewed	NA|78aa|up_0|NZ_CP047801.1_946449_946683_-	PRK00982, acpP, acyl carrier protein; Provisional	NA|245aa|down_0|NZ_CP047801.1_946988_947723_-	PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Validated	NA|309aa|down_1|NZ_CP047801.1_947715_948642_-	COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]	NA|329aa|down_2|NZ_CP047801.1_948634_949621_-	PRK05331, PRK05331, phosphate acyltransferase PlsX	NA|191aa|down_3|NZ_CP047801.1_949625_950198_-	PRK04424, PRK04424, transcription factor FapR	cas3|687aa|down_4|NZ_CP047801.1_950400_952461_-	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional	NA|549aa|down_5|NZ_CP047801.1_952650_954297_-	COG1461, COG1461, Predicted kinase related to dihydroxyacetone kinase [General function prediction only]	NA|125aa|down_6|NZ_CP047801.1_954311_954686_-	COG1302, COG1302, Uncharacterized protein conserved in bacteria [Function unknown]	NA|63aa|down_7|NZ_CP047801.1_955128_955317_+	PRK00359, rpmB, 50S ribosomal protein L28; Reviewed	NA|214aa|down_8|NZ_CP047801.1_955697_956339_-	COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism]	NA|215aa|down_9|NZ_CP047801.1_956345_956990_-	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]
GCF_009912795.1_ASM991279v1	NZ_CP047801	Staphylococcus aureus strain UP_248 chromosome, complete genome	4	1249892-1249977	3	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	CCAACTTGCACATTATTGTAAGCTGGCTTT	30	1	2	1249922-1249947|1249922-1249947	NZ_CP047801.1_2808416-2808441|NZ_CP047801.1_2868500-2868525	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA	NA|301aa|up_9|NZ_CP047801.1_1233926_1234829_-	COG0179, MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]	NA|1218aa|up_8|NZ_CP047801.1_1234994_1238648_-	TIGR02785, ATP-dependent_helicase/nuclease_subunit_A, helicase-exonuclease AddAB, AddA subunit, Firmicutes type	NA|1159aa|up_7|NZ_CP047801.1_1238648_1242125_-	TIGR02773, ATP-dependent_helicase/deoxyribonuclease_subunit_B, helicase-exonuclease AddAB, AddB subunit	NA|192aa|up_6|NZ_CP047801.1_1242284_1242860_-	TIGR02227, Inactive_signal_peptidase_IA	NA|175aa|up_5|NZ_CP047801.1_1242875_1243400_-	TIGR02227, Inactive_signal_peptidase_IA	NA|192aa|up_4|NZ_CP047801.1_1243404_1243980_-	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|444aa|up_3|NZ_CP047801.1_1244305_1245637_-	PRK14097, pgi, glucose-6-phosphate isomerase; Provisional	NA|402aa|up_2|NZ_CP047801.1_1245987_1247193_+	PRK00509, PRK00509, argininosuccinate synthase; Provisional	NA|460aa|up_1|NZ_CP047801.1_1247182_1248562_+	PRK00855, PRK00855, argininosuccinate lyase; Provisional	NA|310aa|up_0|NZ_CP047801.1_1248803_1249733_+	cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins	NA|415aa|down_0|NZ_CP047801.1_1250127_1251372_-	COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]	NA|397aa|down_1|NZ_CP047801.1_1251480_1252671_-	PRK04073, rocD, ornithine--oxo-acid transaminase; Provisional	NA|376aa|down_2|NZ_CP047801.1_1252978_1254106_-	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4	NA|126aa|down_3|NZ_CP047801.1_1254467_1254845_-	COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	NA|198aa|down_4|NZ_CP047801.1_1255259_1255853_-	cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain	NA|128aa|down_5|NZ_CP047801.1_1255916_1256300_+	pfam08810, KapB, Kinase associated protein B	NA|802aa|down_6|NZ_CP047801.1_1256430_1258836_+	PRK12645, PRK12645, monovalent cation/H+ antiporter subunit A; Reviewed	NA|143aa|down_7|NZ_CP047801.1_1258828_1259257_+	PRK12573, PRK12573, Na(+)/H(+) antiporter subunit B	NA|110aa|down_8|NZ_CP047801.1_1259268_1259598_+	PRK08600, PRK08600, putative monovalent cation/H+ antiporter subunit C; Reviewed	NA|499aa|down_9|NZ_CP047801.1_1259590_1261087_+	PRK07691, PRK07691, putative monovalent cation/H+ antiporter subunit D; Reviewed
GCF_009912795.1_ASM991279v1	NZ_CP047801	Staphylococcus aureus strain UP_248 chromosome, complete genome	5	1299020-1299099	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	GGGCCCCAACATAGAAGCTGACGG	24	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA|126aa|down_2|NZ_CP047801.1_1302838_1303216_-	NA|414aa|up_9|NZ_CP047801.1_1289339_1290581_-	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|436aa|up_8|NZ_CP047801.1_1290695_1292003_-	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|254aa|up_7|NZ_CP047801.1_1292100_1292862_-	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|284aa|up_6|NZ_CP047801.1_1293189_1294041_+	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|65aa|up_5|NZ_CP047801.1_1294274_1294469_-	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|274aa|up_4|NZ_CP047801.1_1295284_1296106_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|232aa|up_3|NZ_CP047801.1_1296123_1296819_-	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|342aa|up_2|NZ_CP047801.1_1296811_1297837_-	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|99aa|up_1|NZ_CP047801.1_1298086_1298383_-	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains	NA|129aa|up_0|NZ_CP047801.1_1298375_1298762_-	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|221aa|down_0|NZ_CP047801.1_1299876_1300539_-	COG2226, UbiE, Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]	NA|244aa|down_1|NZ_CP047801.1_1301047_1301779_+	pfam00398, RrnaAD, Ribosomal RNA adenine dimethylase	NA|126aa|down_2|NZ_CP047801.1_1302838_1303216_-	NA	NA|631aa|down_3|NZ_CP047801.1_1303222_1305115_-	cd01187, INT_tnpB_C_Tn554, Putative Transposase B from transposon Tn554, C-terminal catalytic domain	NA|362aa|down_4|NZ_CP047801.1_1305111_1306197_-	cd01186, INT_tnpA_C_Tn554, Putative Transposase A from transposon Tn554, C-terminal catalytic domain	NA|207aa|down_5|NZ_CP047801.1_1306298_1306919_-	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|127aa|down_6|NZ_CP047801.1_1307096_1307477_-	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|119aa|down_7|NZ_CP047801.1_1307634_1307991_-	cd03036, ArsC_like, Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC	NA|107aa|down_8|NZ_CP047801.1_1308134_1308455_+	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains	NA|180aa|down_9|NZ_CP047801.1_1308604_1309144_-	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA
GCF_009912795.1_ASM991279v1	NZ_CP047801	Staphylococcus aureus strain UP_248 chromosome, complete genome	6	1364079-1364163	5	CRISPRCasFinder	no	cas3	DEDDh,csa3,cas3,DinG,WYL	Unclear	TTCTACAGGCAATGCAAGTTGGGGTG	26	1	2	1364105-1364137|1364105-1364137	NZ_CP047801.1_2606508-2606476|NZ_CP047801.1_1124107-1124139	NA	1	1	Unclear	DEDDh,csa3,cas3,DinG,WYL	NA,NA|33aa|down_1|NZ_CP047801.1_1365623_1365722_-	NA|312aa|up_9|NZ_CP047801.1_1351232_1352168_-	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|480aa|up_8|NZ_CP047801.1_1352234_1353674_-	sd00008, TPR_YbbN, C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs	NA|162aa|up_7|NZ_CP047801.1_1353681_1354167_-	cd04647, LbH_MAT_like, Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins	NA|281aa|up_6|NZ_CP047801.1_1354174_1355017_-	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|311aa|up_5|NZ_CP047801.1_1355022_1355955_-	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|949aa|up_4|NZ_CP047801.1_1356565_1359412_-	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|662aa|up_3|NZ_CP047801.1_1359419_1361405_-	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|79aa|up_2|NZ_CP047801.1_1361673_1361910_-	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|217aa|up_1|NZ_CP047801.1_1361906_1362557_-	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|280aa|up_0|NZ_CP047801.1_1362730_1363570_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|370aa|down_0|NZ_CP047801.1_1364338_1365449_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|33aa|down_1|NZ_CP047801.1_1365623_1365722_-	NA	NA|844aa|down_2|NZ_CP047801.1_1365763_1368295_-	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed	NA|191aa|down_3|NZ_CP047801.1_1368708_1369281_-	COG1544, COG1544, Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]	NA|225aa|down_4|NZ_CP047801.1_1369341_1370016_-	COG1040, ComFC, Predicted amidophosphoribosyltransferases [General function prediction only]	cas3|361aa|down_5|NZ_CP047801.1_1370008_1371091_-	COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]	NA|289aa|down_6|NZ_CP047801.1_1371454_1372321_-	TIGR00762, DegV, EDD domain protein, DegV family	NA|214aa|down_7|NZ_CP047801.1_1372464_1373106_+	COG1739, COG1739, Uncharacterized conserved protein [Function unknown]	NA|352aa|down_8|NZ_CP047801.1_1373269_1374325_-	cd06853, GT_WecA_like, This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins	NA|357aa|down_9|NZ_CP047801.1_1374642_1375713_+	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain
GCF_009912795.1_ASM991279v1	NZ_CP047801	Staphylococcus aureus strain UP_248 chromosome, complete genome	7	1761155-1761310	1	PILER-CR	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TTGGTGTTGGTTGTGGCGATTGCGGTTGTACATTTGGTGAAGGCGG	46	0	0	NA	NA	NA	2	2	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|103aa|up_9|NZ_CP047801.1_1750206_1750515_+,NA|496aa|up_8|NZ_CP047801.1_1750620_1752108_-,NA|40aa|up_4|NZ_CP047801.1_1756048_1756168_+,NA|51aa|down_5|NZ_CP047801.1_1767066_1767219_+,NA|179aa|down_7|NZ_CP047801.1_1770044_1770581_+	NA|103aa|up_9|NZ_CP047801.1_1750206_1750515_+	NA	NA|496aa|up_8|NZ_CP047801.1_1750620_1752108_-	NA	NA|233aa|up_7|NZ_CP047801.1_1752126_1752825_-	PRK13036, PRK13036, superantigen-like protein; Reviewed	NA|411aa|up_6|NZ_CP047801.1_1753207_1754440_-	cd17258, RMtype1_S_Sau13435ORF2165P-TRD1-CR1_like, Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S	NA|519aa|up_5|NZ_CP047801.1_1754432_1755989_-	COG0286, HsdM, Type I restriction-modification system methyltransferase subunit [Defense mechanisms]	NA|40aa|up_4|NZ_CP047801.1_1756048_1756168_+	NA	NA|228aa|up_3|NZ_CP047801.1_1756250_1756934_-	PRK13038, PRK13038, superantigen-like protein; Reviewed	NA|233aa|up_2|NZ_CP047801.1_1757296_1757995_-	PRK13345, PRK13345, superantigen-like protein; Reviewed	NA|232aa|up_1|NZ_CP047801.1_1758335_1759031_-	PRK13346, PRK13346, superantigen-like protein 7; Reviewed	NA|235aa|up_0|NZ_CP047801.1_1759477_1760182_-	PRK13035, PRK13035, superantigen-like protein 5; Reviewed	NA|344aa|down_0|NZ_CP047801.1_1761866_1762898_-	PRK13335, PRK13335, superantigen-like protein; Reviewed	NA|234aa|down_1|NZ_CP047801.1_1763185_1763887_-	PRK13041, PRK13041, superantigen-like protein; Reviewed	NA|227aa|down_2|NZ_CP047801.1_1764169_1764850_-	PRK13037, PRK13037, superantigen-like protein; Reviewed	NA|282aa|down_3|NZ_CP047801.1_1765321_1766167_+	cd05269, TMR_SDR_a, triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs	NA|120aa|down_4|NZ_CP047801.1_1766185_1766545_+	COG3759, COG3759, Predicted membrane protein [Function unknown]	NA|51aa|down_5|NZ_CP047801.1_1767066_1767219_+	NA	NA|109aa|down_6|NZ_CP047801.1_1767476_1767803_+	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|179aa|down_7|NZ_CP047801.1_1770044_1770581_+	NA	NA|514aa|down_8|NZ_CP047801.1_1771050_1772592_-	PRK00074, guaA, GMP synthase; Reviewed	NA|489aa|down_9|NZ_CP047801.1_1772616_1774083_-	PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase; Reviewed
GCF_009912795.1_ASM991279v1	NZ_CP047801	Staphylococcus aureus strain UP_248 chromosome, complete genome	8	2404665-2404923	2,6	PILER-CR,CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TATTGAAGAAGATACAA,GCCAACACCACCGACACCAGAGGTACCA	17,28	0	0	NA	NA	NA:NA	2,2	2	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|67aa|up_0|NZ_CP047801.1_2401951_2402152_+,NA|103aa|down_1|NZ_CP047801.1_2406356_2406665_-,NA|89aa|down_2|NZ_CP047801.1_2406808_2407075_-,NA|41aa|down_8|NZ_CP047801.1_2415396_2415519_-,NA|64aa|down_9|NZ_CP047801.1_2415953_2416145_+	NA|204aa|up_9|NZ_CP047801.1_2390785_2391397_-	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|426aa|up_8|NZ_CP047801.1_2391947_2393225_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|608aa|up_7|NZ_CP047801.1_2393701_2395525_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_6|NZ_CP047801.1_2395663_2396080_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_5|NZ_CP047801.1_2396310_2397003_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|244aa|up_4|NZ_CP047801.1_2397167_2397899_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|227aa|up_3|NZ_CP047801.1_2398085_2398766_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_2|NZ_CP047801.1_2398790_2400344_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_1|NZ_CP047801.1_2400460_2401819_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|67aa|up_0|NZ_CP047801.1_2401951_2402152_+	NA	NA|289aa|down_0|NZ_CP047801.1_2405363_2406230_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|103aa|down_1|NZ_CP047801.1_2406356_2406665_-	NA	NA|89aa|down_2|NZ_CP047801.1_2406808_2407075_-	NA	NA|603aa|down_3|NZ_CP047801.1_2407358_2409167_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|131aa|down_4|NZ_CP047801.1_2409283_2409676_+	cd03425, MutT_pyrophosphohydrolase, The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic pyrophosphate (PPi)	NA|954aa|down_5|NZ_CP047801.1_2409677_2412539_+	COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	NA|258aa|down_6|NZ_CP047801.1_2412845_2413619_+	pfam04507, DUF576, Csa1 family	NA|265aa|down_7|NZ_CP047801.1_2414598_2415393_+	pfam04507, DUF576, Csa1 family	NA|41aa|down_8|NZ_CP047801.1_2415396_2415519_-	NA	NA|64aa|down_9|NZ_CP047801.1_2415953_2416145_+	NA
GCF_009912795.1_ASM991279v1	NZ_CP047801	Staphylococcus aureus strain UP_248 chromosome, complete genome	9	2485177-2485281	7	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TGCATAAGCCTTTCTAGCTCATAAAATCCGCAGAAA	36	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|35aa|up_0|NZ_CP047801.1_2484817_2484922_+,NA|35aa|down_2|NZ_CP047801.1_2487453_2487558_-	NA|453aa|up_9|NZ_CP047801.1_2474775_2476134_+	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase	NA|336aa|up_8|NZ_CP047801.1_2476135_2477143_+	PRK06256, PRK06256, biotin synthase; Validated	NA|372aa|up_7|NZ_CP047801.1_2477120_2478236_+	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|231aa|up_6|NZ_CP047801.1_2478246_2478939_+	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|156aa|up_5|NZ_CP047801.1_2478949_2479417_+	pfam06177, QueT, QueT transporter	NA|326aa|up_4|NZ_CP047801.1_2479468_2480446_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|316aa|up_3|NZ_CP047801.1_2480447_2481395_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|310aa|up_2|NZ_CP047801.1_2481944_2482874_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|438aa|up_1|NZ_CP047801.1_2483409_2484723_-	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|35aa|up_0|NZ_CP047801.1_2484817_2484922_+	NA	NA|289aa|down_0|NZ_CP047801.1_2485421_2486288_+	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|229aa|down_1|NZ_CP047801.1_2486614_2487301_+	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|35aa|down_2|NZ_CP047801.1_2487453_2487558_-	NA	NA|480aa|down_3|NZ_CP047801.1_2487731_2489171_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|260aa|down_4|NZ_CP047801.1_2489291_2490071_+	cd13711, PBP2_Ngo0372_TcyA, Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold	NA|240aa|down_5|NZ_CP047801.1_2490051_2490771_+	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|244aa|down_6|NZ_CP047801.1_2490767_2491499_+	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|417aa|down_7|NZ_CP047801.1_2491595_2492846_-	pfam02388, FemAB, FemAB family	NA|121aa|down_8|NZ_CP047801.1_2493100_2493463_+	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|200aa|down_9|NZ_CP047801.1_2493481_2494081_+	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]
GCF_009912795.1_ASM991279v1	NZ_CP047801	Staphylococcus aureus strain UP_248 chromosome, complete genome	10	2640680-2640760	8	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	CAAATTGGCGGGGCCCCAACATAGA	25	1	6	2640705-2640735|2640705-2640735|2640705-2640735|2640705-2640735|2640705-2640735|2640705-2640735	NZ_CP047801.1_465126-465156|NZ_CP047801.1_1095970-1096000|NZ_CP047801.1_1249986-1249956|NZ_CP047801.1_1294817-1294787|NZ_CP047801.1_82071-82101|NZ_CP047801.1_1350717-1350747	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA|57aa|down_0|NZ_CP047801.1_2640816_2640987_-,NA|84aa|down_5|NZ_CP047801.1_2644127_2644379_-,NA|106aa|down_8|NZ_CP047801.1_2649503_2649821_-,NA|55aa|down_9|NZ_CP047801.1_2650065_2650230_-	NA|202aa|up_9|NZ_CP047801.1_2633576_2634182_+	COG4148, ModC, ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]	NA|335aa|up_8|NZ_CP047801.1_2634349_2635354_+	PRK07688, PRK07688, thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated	NA|169aa|up_7|NZ_CP047801.1_2635382_2635889_+	COG0521, MoaB, Molybdopterin biosynthesis enzymes [Coenzyme metabolism]	NA|165aa|up_6|NZ_CP047801.1_2635890_2636385_-	PRK09364, moaC, cyclic pyranopterin monophosphate synthase MoaC	NA|420aa|up_5|NZ_CP047801.1_2636447_2637707_+	cd00887, MoeA, MoeA family	NA|162aa|up_4|NZ_CP047801.1_2637703_2638189_+	COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]	NA|149aa|up_3|NZ_CP047801.1_2638202_2638649_+	COG0314, MoaE, Molybdopterin converting factor, large subunit [Coenzyme metabolism]	NA|78aa|up_2|NZ_CP047801.1_2638654_2638888_+	cd00754, Ubl_MoaD, ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins	NA|200aa|up_1|NZ_CP047801.1_2638894_2639494_+	PRK00317, mobA, molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed	NA|341aa|up_0|NZ_CP047801.1_2639513_2640536_+	TIGR02666, Cyclic_pyranopterin_monophosphate_synthase, molybdenum cofactor biosynthesis protein A, bacterial	NA|57aa|down_0|NZ_CP047801.1_2640816_2640987_-	NA	NA|117aa|down_1|NZ_CP047801.1_2641112_2641463_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|404aa|down_2|NZ_CP047801.1_2641564_2642776_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|147aa|down_3|NZ_CP047801.1_2642768_2643209_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|255aa|down_4|NZ_CP047801.1_2643371_2644136_+	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|84aa|down_5|NZ_CP047801.1_2644127_2644379_-	NA	NA|422aa|down_6|NZ_CP047801.1_2644767_2646033_+	COG2348, COG2348, Peptidoglycan interpeptide bridge formation enzyme [Cell wall/membrane/envelope biogenesis]	NA|1056aa|down_7|NZ_CP047801.1_2646149_2649317_+	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms]	NA|106aa|down_8|NZ_CP047801.1_2649503_2649821_-	NA	NA|55aa|down_9|NZ_CP047801.1_2650065_2650230_-	NA
GCF_009912795.1_ASM991279v1	NZ_CP047801	Staphylococcus aureus strain UP_248 chromosome, complete genome	11	2680642-2680767	9	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TGATATCAAGGGTTTTGTGAGCTTTCGAGTAAAGAGG	37	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA|61aa|down_1|NZ_CP047801.1_2681661_2681844_+,NA|56aa|down_8|NZ_CP047801.1_2690192_2690360_-	NA|315aa|up_9|NZ_CP047801.1_2670914_2671859_+	PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha; Provisional	NA|123aa|up_8|NZ_CP047801.1_2671875_2672244_+	PRK05591, rplQ, 50S ribosomal protein L17; Validated	NA|523aa|up_7|NZ_CP047801.1_2672496_2674064_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|270aa|up_6|NZ_CP047801.1_2674439_2675249_+	PRK13648, cbiO, cobalt transporter ATP-binding subunit; Provisional	NA|287aa|up_5|NZ_CP047801.1_2675245_2676106_+	PRK13646, cbiO, energy-coupling factor transporter ATPase	NA|269aa|up_4|NZ_CP047801.1_2676095_2676902_+	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|265aa|up_3|NZ_CP047801.1_2676906_2677701_+	PRK00021, truA, tRNA pseudouridine(38-40) synthase TruA	NA|146aa|up_2|NZ_CP047801.1_2677949_2678387_+	PRK09216, rplM, 50S ribosomal protein L13; Reviewed	NA|133aa|up_1|NZ_CP047801.1_2678400_2678799_+	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed	NA|479aa|up_0|NZ_CP047801.1_2679147_2680584_+	COG2865, COG2865, Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]	NA|60aa|down_0|NZ_CP047801.1_2680832_2681012_+	PRK09775, PRK09775, type II toxin-antitoxin system HipA family toxin YjjJ	NA|61aa|down_1|NZ_CP047801.1_2681661_2681844_+	NA	NA|555aa|down_2|NZ_CP047801.1_2682313_2683978_+	PRK08617, PRK08617, acetolactate synthase AlsS	NA|235aa|down_3|NZ_CP047801.1_2684014_2684719_+	COG3527, AlsD, Alpha-acetolactate decarboxylase [Secondary metabolites biosynthesis, transport, and catabolism]	NA|142aa|down_4|NZ_CP047801.1_2685109_2685535_-	pfam03642, MAP, MAP domain	NA|272aa|down_5|NZ_CP047801.1_2685829_2686645_+	cd02605, HAD_SPP, sucrose-phosphatase, similar to Synechocystis sp PCC 6803 SPP	NA|285aa|down_6|NZ_CP047801.1_2686855_2687710_+	pfam01551, Peptidase_M23, Peptidase family M23	NA|809aa|down_7|NZ_CP047801.1_2687769_2690196_-	cd01083, GAG_Lyase, Glycosaminoglycan (GAG) polysaccharide lyase family	NA|56aa|down_8|NZ_CP047801.1_2690192_2690360_-	NA	NA|139aa|down_9|NZ_CP047801.1_2690602_2691019_+	cd01109, HTH_YyaN, Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB
GCF_009912795.1_ASM991279v1	NZ_CP047801	Staphylococcus aureus strain UP_248 chromosome, complete genome	12	2894142-2894231	10	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TGATTGAGAAGTCAGTCGAAAAAC	24	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA|52aa|down_2|NZ_CP047801.1_2894784_2894940_+,NA|68aa|down_3|NZ_CP047801.1_2894924_2895128_+,NA|128aa|down_4|NZ_CP047801.1_2895129_2895513_+,NA|127aa|down_8|NZ_CP047801.1_2898798_2899179_+	NA|45aa|up_9|NZ_CP047801.1_2883643_2883778_+	PRK14752, PRK14752, delta-lysin family phenol-soluble modulin	NA|523aa|up_8|NZ_CP047801.1_2884143_2885711_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|262aa|up_7|NZ_CP047801.1_2886043_2886829_-	cd07583, nitrilase_5, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases)	NA|209aa|up_6|NZ_CP047801.1_2887189_2887816_-	COG3560, FMR2, Predicted oxidoreductase related to nitroreductase [General function prediction only]	NA|405aa|up_5|NZ_CP047801.1_2888012_2889227_+	PRK10819, PRK10819, transport protein TonB; Provisional	NA|248aa|up_4|NZ_CP047801.1_2889251_2889995_-	pfam02517, Abi, CAAX protease self-immunity	NA|95aa|up_3|NZ_CP047801.1_2890169_2890454_+	PRK00364, groES, co-chaperonin GroES; Reviewed	NA|539aa|up_2|NZ_CP047801.1_2890529_2892146_+	PRK00013, groEL, chaperonin GroEL; Reviewed	NA|391aa|up_1|NZ_CP047801.1_2892214_2893387_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|225aa|up_0|NZ_CP047801.1_2893400_2894075_-	pfam13443, HTH_26, Cro/C1-type HTH DNA-binding domain	NA|73aa|down_0|NZ_CP047801.1_2894247_2894466_+	smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|106aa|down_1|NZ_CP047801.1_2894470_2894788_+	TIGR01764, Probable_excisionase, DNA binding domain, excisionase family	NA|52aa|down_2|NZ_CP047801.1_2894784_2894940_+	NA	NA|68aa|down_3|NZ_CP047801.1_2894924_2895128_+	NA	NA|128aa|down_4|NZ_CP047801.1_2895129_2895513_+	NA	NA|106aa|down_5|NZ_CP047801.1_2895513_2895831_+	pfam07342, DUF1474, Protein of unknown function (DUF1474)	NA|290aa|down_6|NZ_CP047801.1_2895894_2896764_+	smart00942, PriCT_1, Primase C terminal 1 (PriCT-1)	NA|570aa|down_7|NZ_CP047801.1_2896777_2898487_+	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]	NA|127aa|down_8|NZ_CP047801.1_2898798_2899179_+	NA	NA|214aa|down_9|NZ_CP047801.1_2899175_2899817_+	pfam16560, SAPI, Putative mobile pathogenicity island
